As many of you may know, I have been examining how mRNAs are transported and localized within the cell and how the regulation of mRNA metabolism contributes to gene expression. From data accumulated recently within the "RNA Field", we know that transcription in eukaryotic cells is very sloppy - that is, a plethora of different RNA transcripts are generated from seemingly random pieces of DNA. As I explained in a recent post, some of this background transcription seems to play a role in regulating how the DNA is packed and thus allows for a tighter control of RNA production from protein coding…
... I have two simple requests: Stop asking people if they "believe in evolution". Every time I hear some dumb ass politician or right wing theological nut say "I don't believe in evolution", it makes me cringe. Evolution is not some magical mystical process that you take on faith. Do you ever hear the question "do you believe in algebra?" Instead pose the question "do you understand how evolution works?" Go and read The Origin of Species by Natural Selection and The Voyage of the Beagle. These are simply must reads, especially for anyone in the life sciences. Now I can hear many of you…
You take out your scissors and start cutting. (A photo of baymate working on supplemental figure 12 of Ward et al., PNAS 2007.) To be honest, we didn't know what to make of the final arts & crafts product, a floppy ABC transporter that can be shifted into various conformations, each of which is suppose to represent a different nucleotide-bound state. (You'll also note that this paper was resubmitted due to an infamous error.)
As you know, I'll be leaving the US in the middle of the year to head up north to my native land where I'll be setting up my new lab. Having lived in both the US and Canada, I am in a good position to evaluate both societies. My basic conclusion? America you have a lot to learn from your northern brothers and sisters. It is really frustrating being down here and listening to Americans (especially those on the right) dismiss the concept of public institutions. What do you end up with? A country that is rotting from within. Fortunately things may change for the better. Money from the upcoming…
Bloggers like to talk about how nasty the Main Stream Media is (I'm looking at you physioprof). And although I agree that there are MANY problems, I think that the fifth estate makes a real contribution to our public discourse. Now unlike what others have written, I am not talking about science journalism, a branch of that discipline mostly filled with dilettantes who write trite articles about their misconceptions about the latest research, or the opinion of political pundits (Washington insiders who spin any and every bit of news into some pro-ideology narrative), but the real news…
I just listened to journalist and historian Gwynne Dyer discus what's to come in the not so distant future due to accelerated climate change. The quick summary? The rate of climate change is very fast, the development of technology (good and bad) may be even faster, but the rate of cultural change needed to accommodate these developments is slow and the political will to enact needed reforms may be the slowest of all (although not as slow as evolution, the gradual change that rewires the genomes of most of the organic beings that must cope with our ever more rapidly changing world). What…
... strike again! It's crazy but Boston (and Brookline in particular) is full of wild turkeys. Every once in a while you bump into a gang (or a gobble) of them. Baymate knew of one living near her in Washington Square. One day as one lady left Starbucks, baymate's turkey spotted her and proceeded to chase her down the block. The lady in question was heard screaming on her cell phone, "I have had a shitty day, my morning was bad and now there's a turkey chasing me down the street". Needless to say, baymate fell in love with this turkey. It became a fixture of the neighborhood. Then after a few…
Wow, last week was memorable. Not only did I sign my contract with the University of Toronto, but it appears as if my super duper theory that I thought I had killed, might have been resuscitated. To remind you, the last time I wrote about my trials and tribulations, I thought that I had ruled out my super duper theory because of a simple straight forward experiment. The experiment involved microinjecting a dominant negative protein that blocks a complex from working. What I failed to tell you is that I was waiting for my positive control, a protein whose distribution would be altered if that…
Yes, now that I've received the contract and signed it, I'll officially announce what some of you already know - effective July 1st 2009, I will be a faculty member in the Department of Biochemistry at the University of Toronto. One of my "first acts" will be to collect a little payment from Larry Moran.
From the AAAS: The three agencies highlighted in the America COMPETES Act of 2007 and President Bush's American Competitiveness Initiative (ACI) would do extremely well in the stimulus appropriations bill. The National Science Foundation (NSF) would receive $3.0 billion; the Department of Energy's Office of Science (DOE OS) would receive $2.0 billion; and Commerce's National Institute of Standards and Technology (NIST) would receive $520 million; nearly all of these supplementals are for R&D activities. The $5.5 billion allocated to these three agencies would finally put all three budgets…
I just saw this video on Biocurious: And I have to agree with Dobbs, postdocs are underpaid largely due to an oversupply of foreign PhDs (and yes, I am a foreigner, although I received my PhD here in the US). This is why women drop out of science, this is why there most blogs written by postdocs are filled with complaints. And yes, this is why that old argument that Americans are just not interested in science is hogwash. But do you really think that the solution is to build bigger walls around the nation? This is America, a nation built on immigration, and now you want to prevent the…
I woke up, got the paper and then read this half baked OpEd by David Brooks, the world's most confused conservative. The thesis of his article: liberalism destroys institutions. Here's the opening paragraph: A few years ago, a faculty committee at Harvard produced a report on the purpose of education. "The aim of a liberal education" the report declared, "is to unsettle presumptions, to defamiliarize the familiar, to reveal what is going on beneath and behind appearances, to disorient young people and to help them to find ways to reorient themselves." He then goes on to describe how important…
Yesterday, I was diligently working on my computer when my brother suddenly appeared on MSN's instant messenger. His engineering firm had recently sent him to Doha, Qatar, to work on a new factory being built near the harbor and I was pleasantly surprised that I could chat with him. Next I was shunted to a "conference chat" where he was conversing with his wife, a first grade teacher in Montreal. Next we were all notified that our cousin Tim, who is currently in Kiev, had signed in to MSN. If that wasn't enough, Tim's little sister Laura, who is in DC working with a law firm that advocates…
This has become a yearly tradition. I usually posted near the end of the year, but this time around I had many "distractions". Better late then never: Click here for a full size version. Previous years:20072006
So this week I tried to gain evidence that supports my supper dupper theory, based on my unexpectedly amazing mass spec results I told you about a few weeks ago. Fortunately I had a staight forward way of testing the implications of these initial findings. And my experiments conclusively demonstrated that this new theory was not right. I forgot about Murphy's laws. So after having busted my own new theory, the question to ask would be am I upset? No way. Although some of the proteins in my unexpectedly amazing mass spec results had nothing to do with the process I am studying (the nuclear…
Hello world. Once upon a time, I had a laptop. As time went on, its hard drive filled up with pdfs, music files and an enormous (well, relatively enormous) operating system. This pattern of exponential expansion continued for a few years until, the imbalance between data and storage capacity, just like the overpopulation of the Norwegian hills by lemmings with prolific breading capabilities, could no longer be sustainable. A change was needed before the impending threat of mass suicide. And so on January 7th, having realized that my data needed more fertile ground to colonize, I bought a new…
Yes it looks like I've abandoned my blog, but to be honest in the past few weeks my world has been rocked, scientifically. You see to be a scientist is to be obsessed. Now like some crazed psychotic individual I will try to explain the nature of this infatuation with my work. This desire to obtain the precious insight into the small part of the natural world that remains the foccus of my studies. It starts about one and a half years ago. You see I had a couple of findings that looked good and I sat on them for a while as I attempted to tackle other problems. This set of data, and the model…
Here I am, in the lab with one last experiment to go before I leave to feast on a Christmas Eve dinner, so while I wait for that last centrifugation step, I'll write a quick post about all these great papers on RNA Polymerase II and chromatin remodelling. As I've said before, if you want to understand what is going on with all of these non-coding RNA transcripts, you have to understand how DNA is organized. If you don't understand how DNA is packed in the typical eukaryotic (i.e. nucleated) cell, please read this:How Transcription Affects Genomic Organization and Vice Versa Then to get you…
This is hard. A few days before Xmass, I have HOT results comming out of the lab, and a major snafu is comming out of that endless reservoir of angst, scientists complaining about science journalists ... and now those science journalists are lashing back. I have to say that I really like George Johnson, but over the weekend, he attacked Abbie (who blogs at ERV here at scienceblogs) for complaining about the current state of science journalism. Now George has made it clear that he didn't mean to be so nasty. But is there something that can be learned from all of this? I don't have the time to…
The lack of posts can be explained by this equation (lab work = 1/updates) so I'll make it up to you with a weekend smorgasbord of links. So today as I sit in my warm cozy snowed-in apartment I present to you the latest edition of Tib Bits. First off, I would like to wish happy birthday to the late great Frank Zappa (yes to the chagrin of my wife, I'm a big fan). And what could be more fitting on a day like today than this song: Next, the big news is the financial turmoil that has now spread to all the academic institutions. Even PhD comics had something to say about it: Here are some other…